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(-) Description

Title :  STRUCTURE OF THE CIF:NEDD8 COMPLEX - YERSINIA PSEUDOTUBERCULOSIS CYCLE INHIBITING FACTOR IN COMPLEX WITH HUMAN NEDD8
 
Authors :  A. Crow, M. Banfield
Date :  17 May 12  (Deposition) - 20 Jun 12  (Release) - 20 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Effector-Host Target Complex, Glutamine Deamidase, Deamidation, Bacterial Effector, Cell Cycle-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Crow, R. K. Hughes, F. Taieb, E. Oswald, M. J. Banfield
The Molecular Basis Of Nedd8 Deamidation By The Bacterial Effector Protein Cif
Proc. Natl. Acad. Sci. Usa 2012
PubMed: search

(-) Compounds

Molecule 1 - CYCLE INHIBITING FACTOR
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: SOLUBL21
    Expression System Taxid: 562
    Fragment: EFFECTOR DOMAIN, UNP RESIDUES 33-288
    Gene: YPK_1971
    Mutation: YES
    Organism Scientific: YERSINIA PSEUDOTUBERCULOSIS
    Organism Taxid: 502800
    Strain: YPIII
 
Molecule 2 - NEDD8
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3) ROSSETTA
    Expression System Taxid: 562
    Gene: NEDD8
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NEDDYLIN, NEURAL PRECURSOR CELL EXPRESSED DEVELOPMENTALLY DOWN-REGULATED PROTEIN 8, NEDD-8, UBIQUITIN-LIKE PROTEIN NEDD8

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:57 , ASN A:60 , VAL A:61 , SER A:108 , SER A:109 , ARG A:111 , HOH A:510BINDING SITE FOR RESIDUE EDO A 301
2AC2SOFTWAREHIS A:226 , GLY A:229 , ILE A:235 , ASP A:236 , HIS A:239 , ILE A:240BINDING SITE FOR RESIDUE EDO A 302
3AC3SOFTWARETHR C:225 , HIS C:226 , ILE C:235 , ASP C:236 , HIS C:239 , ILE C:240BINDING SITE FOR RESIDUE EDO C 301
4AC4SOFTWARELEU C:57 , ASN C:60 , VAL C:61 , SER C:108 , ARG C:111 , HOH C:530BINDING SITE FOR RESIDUE EDO C 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4F8C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4F8C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4F8C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4F8C)

(-) Exons   (0, 0)

(no "Exon" information available for 4F8C)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:249
                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh.hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh........hhhhhhhhhhhhhhh..............hhhhhhhhhhh.....eeeeeeee....eeeeeee........eeeee............hhhhhhhhh....eehhhhhhhhhhh.....hhhhhhhhhh...hhhhhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f8c A  40 NPSIQHVQDFATLSARSLRANVLLNSDDHSVPIHAKNPSELLEAIDNNISQTAQDWGVSIQEVEVILGSSKRIIEPVAGVTANTIMKLFLDNDIFSYSFEKGQSLSLSQLQERLASLPAHKNFILRVNDGGLGHAYVIDFPATTNPSRDAFLYQSDLGEGVTREVRFEDWMTQKASHPISLDDINTHFIGIAQDQIDLAHIAKLFDVDGNVKMLRADHLISHKTSEFNFQLFEYDLKNLENNMSIIKTH 288
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279         


Chain B from PDB  Type:PROTEIN  Length:74
                                                                                                          
               SCOP domains d4f8cb_ B: Nedd8                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhhhheeee..ee.....hhhhhh.....eeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 4f8c B   1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLALR  74
                                    10        20        30        40        50        60        70    


Chain C from PDB  Type:PROTEIN  Length:248
                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh.hhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh........hhhhhhhhhhhhhhh......hhhhh...hhhhhhhhhh......eeeeeeee....eeeeeee..........eee............hhhhhhhhh.....hhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4f8c C  40 NPSIQHVQDFATLSARSLRANVLLNSDDHSVPIHAKNPSELLEAIDNNISQTAQDWGVSIQEVEVILGSSKRIIEPVAGVTANTIMKLFLDNDIFSYSFEKGQSLSLSQLQERLASLPAHKNFILRVNDGGLGHAYVIDFPATTNPSRDAFLYQSDLGEGVTREVRFEDWMTQKASHPISLDDINTHFIGIAQDQIDLAHIAKLFDVDGNVKMLRADHLISHKTSEFNFQLFEYDLKNLENNMSIIKT 287
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279        


Chain D from PDB  Type:PROTEIN  Length:73
                                                                                                         
               SCOP domains d4f8cd_ D: Nedd8                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhhhheeee..ee......hhhhh.....eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 4f8c D   1 MLIKVKTLTGKEIEIDIEPTDKVERIKERVEEKEGIPPQQQRLIYSGKQMNDEKTAADYKILGGSVLHLVLAL  73
                                    10        20        30        40        50        60        70
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4F8C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4F8C)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)

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  A0A0H3B1Q8_Y | A0A0H3B1Q8
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  NEDD8_HUMAN | Q15843
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NEDD8_HUMAN | Q15843: 1ndd 1r4m 1r4n 1xt9 2bkr 2ko3 2n7k 2nvu 3dbh 3dbl 3dbr 3dqv 3gzn 4fbj 4hcp 4p5o

(-) Related Entries Specified in the PDB File

4fbj